Fast download BLAST databases from NCBI

Database files (volumes) are downloaded in parallel: number of threads to use is determined automatically. MD5 checksum is verified and the database volume extracted upon download. Database volumes are not downloaded in a particular order. The volumes are updated if a newer version is available on the server, or re-downloaded if corrupt. Aborted downloads are safely resumed.

ncbi-blast-dbs is faster than NCBI's update_blastdb.pl. But unlike update_blastdb.pl, which is a pure Perl script, ncbi-blast-dbs delegates download and checksum verification to wget and md5sum and is thus not as universal.

Installation

gem install ncbi-blast-dbs

Note for macOS users

If md5sum command is not present, you can install it using Homebrew:

brew install md5sha1sum

Usage

List available BLAST databases

ncbi-blast-dbs

Download all volumes of a BLAST database

ncbi-blast-dbs nt nr

Databases are downloaded one after the other. Volumes of each database are downloaded in parallel. Downloads are placed in the current directory.

NCBI expects users to submit their email address when downloading data from their FTP server. To comply with that, download as:

email="my email address here" ncbi-blast-dbs nr